Hey Alessandro,
You are correct. You could connect your Strobe to PFI0. Since the acquisition will be hardware timed, in our DAQ Assistant we want to set the Acquisition Mode to 1 Sample (HW Timed), N Samples, or Continuous Samples depending on your application. You will then want to select the Advanced Timing tab and select your Sample Clock Type as External and the Clock Source as PFI0. I also attached a tutorial on the DAQ Assistant in LabWindows/CVI.
Using the DAQ Assistant in LabWindows/CVI
http://zone.ni.com/devzone/cda/tut/p/id/4650
Regards,
Chris Delvizis
National Instruments